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Question about startup-script and windows folder structure

Since a time back, I have merged to a system where I put all the scripts I download from ScriptSpot to the localappdata-folder:

%localappdata%\Autodesk\3dsMax\2014 - 64bit\ENU

The benefits are:
- Easy overview
- Easy backup possibilities, since its a single place
- Better ordering (with due all respect to the original script developer's choice of folder structure)

As an introduction, this is how my structure looks like

.\ENU\scripts -- here is where I put folders with .ms or .mse files the way they came from the script developer

.\ENU\scripts\_Haider -- here I put all the loose .ms or .mse files that run out of the box

.\ENU\scripts\startup\Haider -- here I put my own files. I intentionally created a subfolder so I know what is added by me, where everything else in the startup folder is added by others

.\ENU\usericons -- as usual

.\ENU\usermacros\Haider -- Here I put every mcr file I get from the developer. I intentionally created a subfolder so I know what is added by me, where everything else in the usermacros folder is added by others

My problem about the startup folder
Usually, the scripts I have in my startup\Haider folder works great. But there seem to be some files that doesnt work unless I put them into the max-folder\stdplugs\stdscripts. Pprobably the effect would be the same in max-folder\scripts\Startup, but the whole idea was to centralize all the script's locations.

One of them is the mb_shortcuts_fn.ms file (source) and another is autoVP.ms (source)

So it means that those scipts are designed like that, they need to be launched _really_ early to work, hence %localappdata%...\startup is too late?

I suspected it was like that, but wanted a confirmation by a trained eye, who maybe knows those script I mentioned or could look into them to know what they are and then explain to me why they wont work at all in the user startup scripts directory...

Is it even possible to modify the scripts to work from user startup scripts directory or are there things that can never work if they are loaded "too late"?